I am struggling to generate a symmdef file for a helical model and I am hoping someone can help.
The helical parameters are as follows: rise = 17 Angstrom with 4.674 subunits per turn. The helix is apolar i.e. the ends of the helix are the same as related by 180 degree rotation. The repeating unit is a dimer with C2 symmetry. In the attached pdb (ca only to avoid upload limit) the A and B chains form the dimer which is related to the next C/D pair by the helical symmetry I mentioned.
I can generate a symmdef file and correct model for one of the monomers of the dimer using the following command:
make_symmdef_file.pl -m HELIX -a A -b C -p 4monomers_finetuned.pdb
This generates a helix comprising chain A, chain C … and 4 subunits in either direction. However, when I try to include the C2 symmetric neighbour of chain A using the “-I” flag it fails using this command:
make_symmdef_file.pl -m HELIX -a A -b C –i B -p 4monomers_finetuned.pdb
The result is a pdb with all the chains aligned along the helical axis in a nonsensical fashion i.e. overlapping subunits.
Is there something I am doing wrong?